[English] 日本語
Yorodumi
- PDB-5csb: The crystal structure of beta2-microglobulin D76N mutant at room ... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 5csb
TitleThe crystal structure of beta2-microglobulin D76N mutant at room temperature
ComponentsBeta-2-microglobulin
KeywordsIMMUNE SYSTEM / Beta-2 Microglobulin / amyloidosis / room temperature / Immunoglobulin-like
Function / homology
Function and homology information


negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion ...negative regulation of receptor binding / early endosome lumen / Nef mediated downregulation of MHC class I complex cell surface expression / DAP12 interactions / transferrin transport / cellular response to iron ion / Endosomal/Vacuolar pathway / Antigen Presentation: Folding, assembly and peptide loading of class I MHC / peptide antigen assembly with MHC class II protein complex / cellular response to iron(III) ion / MHC class II protein complex / negative regulation of forebrain neuron differentiation / antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent / ER to Golgi transport vesicle membrane / peptide antigen assembly with MHC class I protein complex / regulation of iron ion transport / regulation of erythrocyte differentiation / HFE-transferrin receptor complex / response to molecule of bacterial origin / MHC class I peptide loading complex / T cell mediated cytotoxicity / positive regulation of T cell cytokine production / antigen processing and presentation of endogenous peptide antigen via MHC class I / antigen processing and presentation of exogenous peptide antigen via MHC class II / positive regulation of immune response / MHC class I protein complex / positive regulation of T cell activation / peptide antigen binding / positive regulation of receptor-mediated endocytosis / negative regulation of neurogenesis / cellular response to nicotine / positive regulation of T cell mediated cytotoxicity / multicellular organismal-level iron ion homeostasis / specific granule lumen / phagocytic vesicle membrane / recycling endosome membrane / Interferon gamma signaling / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / negative regulation of epithelial cell proliferation / MHC class II protein complex binding / Modulation by Mtb of host immune system / late endosome membrane / sensory perception of smell / positive regulation of cellular senescence / tertiary granule lumen / DAP12 signaling / T cell differentiation in thymus / negative regulation of neuron projection development / ER-Phagosome pathway / protein refolding / early endosome membrane / protein homotetramerization / amyloid fibril formation / intracellular iron ion homeostasis / learning or memory / endoplasmic reticulum lumen / Amyloid fiber formation / Golgi membrane / lysosomal membrane / external side of plasma membrane / focal adhesion / Neutrophil degranulation / SARS-CoV-2 activates/modulates innate and adaptive immune responses / structural molecule activity / endoplasmic reticulum / Golgi apparatus / protein homodimerization activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane / cytosol
Similarity search - Function
Beta-2-Microglobulin / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily ...Beta-2-Microglobulin / : / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulin-like fold / Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Beta-2-microglobulin
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.719 Å
Authorsde Rosa, M. / Mota, C.S. / de Sanctis, D. / Bolognesi, M. / Ricagno, S.
CitationJournal: Nat Commun / Year: 2018
Title: Conformational dynamics in crystals reveal the molecular bases for D76N beta-2 microglobulin aggregation propensity.
Authors: Le Marchand, T. / de Rosa, M. / Salvi, N. / Sala, B.M. / Andreas, L.B. / Barbet-Massin, E. / Sormanni, P. / Barbiroli, A. / Porcari, R. / Sousa Mota, C. / de Sanctis, D. / Bolognesi, M. / ...Authors: Le Marchand, T. / de Rosa, M. / Salvi, N. / Sala, B.M. / Andreas, L.B. / Barbet-Massin, E. / Sormanni, P. / Barbiroli, A. / Porcari, R. / Sousa Mota, C. / de Sanctis, D. / Bolognesi, M. / Emsley, L. / Bellotti, V. / Blackledge, M. / Camilloni, C. / Pintacuda, G. / Ricagno, S.
History
DepositionJul 23, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Aug 10, 2016Provider: repository / Type: Initial release
Revision 1.1Jun 27, 2018Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.3Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Beta-2-microglobulin


Theoretical massNumber of molelcules
Total (without water)11,8781
Polymers11,8781
Non-polymers00
Water66737
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area6600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)56.000, 29.320, 63.678
Angle α, β, γ (deg.)90.00, 98.57, 90.00
Int Tables number5
Space group name H-MI121

-
Components

#1: Protein Beta-2-microglobulin


Mass: 11878.372 Da / Num. of mol.: 1 / Fragment: UNP residues 21-119 / Mutation: D76N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: B2M, CDABP0092, HDCMA22P / Production host: Escherichia coli (E. coli) / References: UniProt: P61769
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 37 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION

-
Sample preparation

CrystalDensity Matthews: 2.18 Å3/Da / Density % sol: 43.47 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 30% PEG 4000, 0.1M sodium acetate, 15% glycerol, 0.2M ammonium acetate

-
Data collection

DiffractionMean temperature: 293 K / Ambient temp details: room temperature
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.98 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 21, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.719→45.045 Å / Num. obs: 10186 / % possible obs: 92.3 % / Redundancy: 2.2 % / Rmerge(I) obs: 0.056 / Net I/σ(I): 7.6
Reflection shellResolution: 1.719→1.81 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 2.2 / % possible all: 93

-
Processing

Software
NameVersionClassification
PHENIX1.8.4_1496refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4FXL

4fxl


Resolution: 1.719→45.045 Å / SU ML: 0.21 / Cross valid method: FREE R-VALUE / σ(F): 1.5 / Phase error: 23.23 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2234 1017 9.99 %
Rwork0.1819 --
obs0.1861 10182 91.45 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.719→45.045 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms837 0 0 37 874
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009937
X-RAY DIFFRACTIONf_angle_d1.2931283
X-RAY DIFFRACTIONf_dihedral_angle_d13.365371
X-RAY DIFFRACTIONf_chiral_restr0.05136
X-RAY DIFFRACTIONf_plane_restr0.005168
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.719-1.80970.27771450.25121309X-RAY DIFFRACTION92
1.8097-1.9230.24731390.21211270X-RAY DIFFRACTION90
1.923-2.07150.26071460.18571310X-RAY DIFFRACTION91
2.0715-2.280.24091460.1931309X-RAY DIFFRACTION92
2.28-2.60990.24991420.17991281X-RAY DIFFRACTION90
2.6099-3.2880.22961470.18861327X-RAY DIFFRACTION92
3.288-45.0450.19171520.16431359X-RAY DIFFRACTION92
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
17.51-0.1848-5.55854.37830.42844.1028-0.0205-0.17590.3989-0.24630.3103-0.4824-0.18790.8025-0.18490.1469-0.03220.03060.15490.01180.2308-8.24564.7056-17.2191
22.643-0.29640.78781.16210.50266.14-0.0356-0.30010.31980.11330.1141-0.0442-0.183-0.1452-0.01230.11790.0067-0.00780.1324-0.03510.2069-9.075214.97091.0645
34.53670.7955-4.56294.3503-1.19034.7790.51640.52720.52390.1674-0.20570.2789-0.6339-0.7327-0.27010.26840.0246-0.06080.33290.00030.3079-9.921417.8412-5.1534
43.2820.0101-0.73872.41652.17828.1750.036-0.55420.05590.3405-0.16350.17750.4046-0.49630.11530.1355-0.00270.01240.20030.00990.2179-14.944411.34181.5378
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 0 through 5 )
2X-RAY DIFFRACTION2chain 'A' and (resid 6 through 41 )
3X-RAY DIFFRACTION3chain 'A' and (resid 42 through 61 )
4X-RAY DIFFRACTION4chain 'A' and (resid 62 through 99 )

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more